Variant chr6-16290617-T-TAC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_006877.4(GMPR):c.855_856dup(p.Arg286ThrfsTer28) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00192 in 1,613,838 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0019 ( 3 hom. )

Consequence

GMPR
NM_006877.4 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 9.32

Variant links:

Genes affected

GMPR (HGNC:4376): (guanosine monophosphate reductase) This gene encodes an enzyme that catalyzes the irreversible and NADPH-dependent reductive deamination of GMP to IMP. The protein also functions in the re-utilization of free intracellular bases and purine nucleosides.[provided by RefSeq, Oct 2009]

GMPR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 6-16290617-T-TAC is Benign according to our data. Variant chr6-16290617-T-TAC is described in ClinVar as [Likely_benign]. Clinvar id is 731036.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GMPR	NM_006877.4 linkuse as main transcript	c.855_856dup	p.Arg286ThrfsTer28	frameshift_variant	8/9	ENST00000259727.5
GMPR	XM_047418656.1 linkuse as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
GMPR	ENST00000259727.5 linkuse as main transcript	c.855_856dup	p.Arg286ThrfsTer28	frameshift_variant	8/9	1	NM_006877.4	P1
GMPR	ENST00000540478.1 linkuse as main transcript	n.675_676dup		non_coding_transcript_exon_variant	1/2	2
GMPR	ENST00000543191.5 linkuse as main transcript	n.350_351dup		non_coding_transcript_exon_variant	3/4	2
GMPR	ENST00000544145.1 linkuse as main transcript	n.209_210dup		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes

AF:

0.00204

AC:

310

AN:

152084

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000197

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00453

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00363

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.00172

AC:

432

AN:

251434

Hom.:

AF XY:

0.00169

AC XY:

230

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.000123

Gnomad AMR exome

AF:

0.000116

Gnomad ASJ exome

AF:

0.0000992

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00365

Gnomad NFE exome

AF:

0.00293

Gnomad OTH exome

AF:

0.00212

GnomAD4 exome

AF:

0.00191

AC:

2795

AN:

1461636

Hom.:

Cov.:

AF XY:

0.00188

AC XY:

1368

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.000268

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00423

Gnomad4 NFE exome

AF:

0.00220

Gnomad4 OTH exome

AF:

0.00157

GnomAD4 genome

AF:

0.00204

AC:

310

AN:

152202

Hom.:

Cov.:

AF XY:

0.00196

AC XY:

146

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.000241

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00453

Gnomad4 NFE

AF:

0.00363

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.00339

Hom.:

Bravo

AF:

0.00131

EpiCase

AF:

0.00158

EpiControl

AF:

0.00142

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over